1. Field of the Invention
The present invention relates generally to a computer-implemented image processing method for processing a plurality of similar images, and more particularly to a computer-implemented image processing method for warping a plurality of similar gel electrophoresis images in order to bring the images or portions thereof into registration with one another. The present invention further relates to a computer adapted to perform the image processing method.
2. Description of the Background Art
The term registration is often used with respect to printing processes to indicate the correct relation or exact superimposition between colors in color printing. In the present invention, the term registration refers to superimposition and alignment of features in a plurality of images where the features include a common pattern, or portions of a common pattern in each image, the pattern being identifiable by the naked eye and/or computer.
The term image processing is generally considered to mean the computerized manipulation of images or sets of images in order to facilitate the extraction of information, either by visual inspection or by automated measurement. Image processing is commonly used to enhance the usefulness of an image by changing the intensity, contrast, borders, size, placement, etc., of an image or features in the image. Image processing is also used to identify, locate and/or measure features represented within the image.
An image processing algorithm is a set of steps that may be automatically and rapidly applied to an image by a computer. Computers and digital electronics have brought about a multitude of ways in which images may be processed and manipulated. Numerous mathematical algorithms may be used, and image data may be processed on the level of individual pixels (in computer terms, a pixel is a basic picture element and is the smallest unit of visual information in an image). Image warping is a type of image processing which deals with geometric transformations to image features.
Warping refers to a process of applying geometric corrections to modify the shape of features and to change their spatial relationships. Another term used for a warping process is rubber-sheeting because the warping process can be likened to stretching a rubber sheet wherein portions of one or more images are stretched or shrunk in order to bring the spots on all the images into registration with one another and still maintain relative positional relationships between the spots.
One area in which computer-implemented image processing is useful is in the area of macromolecular analysis. Modern medicine has made great advances through the study of body chemistry and cell components. Living tissue is made up of a vast array of macromolecules, or large molecules, which perform a vast array of functions. Macromolecules, their identity, placement, and function, are important for many reasons, including, for example, drug actions and interactions, drug concentrations, body chemistry, DNA and RNA analysis, protein detection, protein generation, etc. Macromolecular analysis is particularly useful in stained gel applications, and may encompass applications such as, for example, protein analysis, DNA analysis, RNA analysis, etc. Large scale automation and computer processing are needed because of the huge numbers of component combinations that must be identified.
Macromolecular analyses often involve one or more electrophoresis steps. Electrophoresis is a process wherein macromolecules suspended in a liquid or gel are subjected to an electrical field, physically separating particles on the basis of inherent electrical charges and/or size. A typical macromolecular analysis has several general steps. First, a test sample containing a test material to be analyzed is prepared. The prepared test sample is then electrophoresed to separate components of the test sample. The electrophoresis separation may be performed in one or more dimensions. A two-dimensional electrophoresis process creates a two-dimensional distribution of components throughout the electrophoresis gel. The electrophoresis is generally followed by a staining step wherein a stain is bonded to a certain type of molecule contained in the macromolecules of the test material. Typical stains include visible and fluorescent stains. In a two-dimensional electrophoresis gel the staining creates a two-dimensional pattern of components. These components generally appear as small (usually elliptical) objects commonly call "spots".
One method and corresponding apparatus for performing two-dimensional electrophoresis is described in U.S. Pat. No. 5,993,627, which is incorporated herein by reference in its entirety.
In repetitious processing of a biological cellular sample using two-dimensional separation techniques, various portions of the cellular material are separated in predictable patterns where the spots of macromolecular material consistently separate and migrate to locations on the gel relative to one another creating a recognizable two-dimensional pattern. For a given type of sample, for instance, proteins from rat liver tissue, a reproducible pattern of spots emerges during the staining process mentioned above. The pattern is mappable in that the approximate location of one spot is predictable relative to the location of other spots.
In a comparison between images of two different gels from similar samples, the pattern will typically be readily recognized. However, if one image is superimposed over the other image, the patterns of spots on the two different gels will not necessarily align with one another. Due to the soft and flexible nature of the gel material, the gels themselves may suffer from physical distortion or shifting of a spot or group of spots in the pattern contained in the image. In other words, various spots or groups of spots of the pattern will be located in the vicinity of their predicted relative location but will not necessarily be in alignment with the recognizable pattern known from another gel. Similarly, images of a single gel taken at different times during a staining process may not be aligned, though distortions will be less than experienced with two images of two different gels.
In order for a computer to process images representing the spots on two or more gel images, and produce meaningful information based upon comparison of two or more gels images, it is advantageous for the images to be brought into registration with one another. Specifically, the recognizable patterns of spots must be brought into alignment with one another in order for a comparison of one spot on a first gel image to be compared to the corresponding spot on other gel images. Therefore, there is a need for computer implemented process for bringing corresponding spots on one gel into registration with spots on one or more other gels. Once a pattern of spots on one gel image is brought into registration with the pattern of spots on another gel image, the computer can make meaningful comparisons between corresponding spots, such as size and density information.
The spots in a pattern may also be analyzed and compared with a known pattern, also referred to as a master pattern. The master pattern is a pattern where previously observed spots have been mapped and may be numbered or indexed for identification. Information concerning the make-up of an indexed spot may or may not be known, however the location of the spot relative to other spots on a gel is known. The indexing specifically identifies a relative location of the spot in the master pattern, and may include further information about the spot such as identification of the specific cellular material concentrated in that spot.
The pattern analysis step is critical, because even if the process is carefully controlled up to this point, a poor quality pattern analysis may yield incorrect, confusing, or misleading results. This is because the size, physical location, and intensity of electrophoresed spots may be used to determine the macromolecular components of a sample under test.
During the above mentioned staining process, due to levels of concentration of material in a particular spot on the gel, and other factors, some spots become very large and the image of that spot may be blurred. For instance, some spots may in fact be several spots that are very close to one another making the distinction between the spots difficult. Therefore, there is a need for a method for determining during the staining process the true nature of an overly large spot.
In macromolecular analysis methods where a carrier, such as a gel slab, is immersed in a developer or stain, individual spots may become visible at different rates, so that over a selected period of time, spots and patterns of spots may appear, darken, and ultimately reach saturation. There is no single point in time that yields optimal visualization for all objects in the image simultaneously. Therefore, there is a need to study a gel at different times in the staining process.